Protein post-translational modification by lysine succinylation: Biochemistry, biological implications, and therapeutic opportunities.

Lysine succinylation (Ksuc) is a novel protein post-translational modification (PTM) wherein a succinyl group modifies a lysine residue. Ksuc leads to significant chemical and structural changes to the modified protein. Recent studies have shown that Ksuc might play an important role in organism physiology and some pathophysiological processes, such as tumorigenesis and metabolic diseases. To provide an understanding of the molecular mechanism and functions of Ksuc in different organisms, we reviewed the current literature about Ksuc, mainly summarizing the research advances in eukaryotes and prokaryotes based on both traditional study methods and site prediction tools. We also discussed inhibitors or activators associated with Ksuc that may contribute to proteomic studies and could be useful in future clinical practice. A deeper understanding of Ksuc may shed new light on life science at the protein level and could lead to novel therapeutic strategies for various diseases.

Characterization and genome analysis of G1 sub-cluster mycobacteriophage Lang.

Phage therapy is revitalized as an alternative to antibiotics therapy against antimicrobials resistant pathogens. Mycobacteriophages are genetically diverse viruses that can specifically infect Mycobacterium genus including Mycobacterium tuberculosis and Mycobacterium smegmatis. Here, we isolated and annotated the genome of a mycobacteriophage Lang, a temperate mycobacteriophage isolated from the soil of Hohhot, Inner Mongolia, China, by using Mycolicibacterium smegmatis mc2 155 as the host. It belongs to the Siphoviridae family of Caudovirales as determined by transmission electron microscopy. The morphological characteristics and certain biological properties of the phage were considered in detail. Phage Lang genomes is 41,487 bp in length with 66.85% GC content and encodes 60 putative open reading frames and belongs to the G1 sub-cluster. Genome annotation indicated that genes for structure proteins, assembly proteins, replications/transcription and lysis of the host are present in function clucters. The genome sequence of phage Lang is more than 95% similar to that of mycobacteriophage Grizzly and Sweets, differing in substitutions, insertions and deletions in Lang. One-step growth curve revealed that Lang has a latent period of 30 min and a outbreak period of 90 min. The short latent period and rapid outbreak mark the unique properties of phage Lang, which can be another potential source for combating M. tuberculosis.

Insertion Mutation of MSMEG_0392 Play an Important Role in Resistance of M. smegmatis to Mycobacteriophage SWU1.

PURPOSE: Phage is a new choice for the treatment of multi-drug-resistant bacteria, and phage resistance is also an issue of concern. SWU1 is a mycobacteriophage, and the mechanism of its resistance remain poorly understood. METHODS: The mutant strains which were stably resistant to SWU1 were screened by transposon mutation library. The stage of phage resistance was observed by transmission electron microscope (TEM). The insertion site of transposon was identified by thermal asymmetric interlaced PCR (TAIL-PCR). The possible relationship between insertion site and phage resistance was verified by gene knockout technique. The fatty acid composition of bacterial cell wall was analyzed by Gas Chromatography-Mass Spectrometer (GC-MS). Through the amplification and sequencing of target genes and gene complement techniques to find the mechanism of SWU1 resistance. RESULTS: The transposon mutant M12 which was stably resistant to mycobacteriophage SWU1 was successfully screened. It was confirmed that resistance occurred in the adsorption stage of bacteriophage. It was verified that the insertion site of the transposon was located in the MSMEG_3705 gene, but after knocking out the gene in the wild type M. smegmatis mc2 155, the resistance of the knockout strain to SWU1 was not observed. Through the amplification and sequencing of the target gene MSMEG_0392, it was found that there was an adenine insertion mutation at position 817. After complementing MSMEG_0392 in M12, it was found that M12 returned to sensitivity to SWU1. CONCLUSION: We confirmed that the resistance of M12 to SWU1 was related to the functional inactivation of MSMEG_0392 and this phenomenon may be caused by the change of cell wall of M. smegmatis.

Mycobacterium Lrp/AsnC family transcriptional factor modulates the arginase pathway as both a sensor and a transcriptional repressor.

L-Arginine is the precursor of nitric oxide (NO), a host immune effector against intracellular pathogens including Mycobacterium tuberculosis (M. tb). Pathogens including M. tb have evolved various strategies targeting arginine to block the production of NO for better survival and proliferation. However, L-arginine metabolism and regulation in Mycobacterium are poorly understood. Here, we report the identification of M. smegmatis MSMEG_1415 (homolog of M. tb Rv2324) as an arginine-responsive transcriptional factor regulating the arginase pathway. In the absence of L-arginine, MSMEG_1415 acts as a repressor to inhibit the transcription of the roc (for arginine, ornithine catabolism) gene cluster, thereby switching off the arginase pathway. Treatment with L-arginine relieves the transcriptional inhibition of MSMEG_1415 on the roc gene cluster to activate the arginase pathway. Moreover, the L-arginine-MSMEG_1415 complex activates the transcription of the roc gene cluster by recognizing and binding a 15-bp palindrome motif, thereby preventing the excess accumulation of L-arginine in M. smegmatis. Physiologically, MSMEG_1415 confers mycobacteria resistance to starvation and fluoroquinolones exposure, suggestive of its important role in M. smegmatis persistence. The results uncover a unique regulatory mechanism of arginine metabolism in mycobacteria and identify M. tb Rv2324 as an attractive candidate target for the design of drugs against tuberculosis.

Gas phase formation of carbon cluster (fullerenes and graphenes)/prebiotic sugar complexes.

Among the constituent molecular classes of proteins and nucleic acids, the presence of Ribose and deoxy-Ribose in space remains unclear. Here, we provide experimental evidence of astronomically related sugar derivatives - carbon cluster (fullerenes and graphenes)/prebiotic sugar complexes - and study their formation processes in the gas phase. The results show that, with PAH cations (dicoronylene, DC, C48H20+)/(2-deoxy-d-Ribose, dR, C5H10O4, and dehydrated 2-deoxy-d-Ribose, DedR, C5H8O3) and fullerene cations (C60+)/(dR and DedR) as the initial molecular precursors, two series of graphene-prebiotic sugar cluster cations (graphene/dR and graphene/DedR, e.g., (dR)Cn+ and (DedR)Cn+) and two series of fullerene-prebiotic sugar cluster cations (fullerene/dR and fullerene/DedR, e.g., (dR)(DedR)2Cn+, (DedR)3Cn+, and (dR)2(DedR)Cn+) are formed through an ion-molecule reaction pathway under the influence of a strong radiation field. The structures of the newly formed complexes and the binding energies of these formation reactions are initially theoretically calculated. These laboratory studies attest to the importance of ion-molecule reaction synthesis routes for the chemical complexity in space, demonstrating that the gas phase interstellar materials could directly lead to the formation of large and complex sugar derivatives in a bottom-up growth process. The chemical evolution in space in which single molecules are transformed into complex molecules produces a wide variety of organic compounds (e.g., carbon cluster (fullerenes and graphenes)/prebiotic sugar complexes). For their astrobiological implications, this opens up aromatic based biogenic chemistry that is available to the parent of PAHs or fullerenes in the interstellar environments.

Clinical characteristics and prognostic factors of male yolk sac tumor: a Surveillance, Epidemiology, and End Results program study.

INTRODUCTION: Yolk sac tumor (YST) is a rare malignant germ cell tumor, which usually affects young males. Because of the low incidence, few studies on YST have been published. In our study, we aim to investigate the clinical characteristics, survival and risk factors of male YST patients based on the Surveillance, Epidemiology, and End Results (SEER) program. METHODS: We identified 569 male YST patients from the SEER-18 database with additional treatment fields. Clinical characteristics, survival and prognostic factors were described in the study. Chi-square tests were applied to analyze categorical and continuous variables between different groups. Univariate and multivariate Cox proportional hazard model were performed to assess the relative impacts of risk factors on cancer-specific survival (CSS) in YST patients. Kaplan-Meier method and the log-rank test were used to analyze differences in survival that were significant. RESULTS: The major primary sites of YST were testis (74.69%), mediastinum (15.47%), retroperitoneum (2.64%) and central nervous system (1.24%). The 3-year and 5-year CSS was 70.0%, 56.5% vs. 97.2%, 96.0% for the mediastinal and testicular YST patients, respectively (p < 0.001). Primary site of mediastinum, distant SEER Summary stage were independent factors of poor prognosis (hazard ratio (HR) = 2.010 (1.094-3.695), p = 0.025; HR = 6.501 (2.294-18.424), p < 0.001, respectively). Receiving surgery was a good prognosis factor for all patients (HR = 0.495 (0.260-0.940), p = 0.032) and for the mediastinal group (p = 0.0019). Being treated with chemotherapy indicated poor outcome in all patients (HR = 3.624 (1.050-12.507), p = 0.042) and in the localized testicular YST patients (p = 0.0077). CONCLUSION: For the first time, our study revealed the primary site distribution of male YST, and summarized the clinical characteristics, survival and prognostic factors based on the SEER database, which provided important epidemiological evidence for clinical practice.

Mycobacterium Von Willebrand factor protein MSMEG_3641 is involved in biofilm formation and intracellular survival.

Aim:Mycobacterium tuberculosis in vitro biofilm is associated with the virulence and persistence capability. Our aim is to delineate factors involved in biofilms development. Materials & methods: We performed transposon mutants screen and found that mutation of MSMEG_3641, a homolog of M. tuberculosis Rv1836c, can change M. smegmatis colony morphology and biofilm. Results: MSMEG_3641 contains a vWA domain that is highly conserved among Mycobacteria. The phenotypes of MSMEG_3641 mutants include disrupted biofilm, weakened migration ability and changed colony morphology. All phenotypes might be contributed to the enhanced cell wall permeability and declined cell aggregation ability. Conclusion: To our knowledge, this is the first report concerning the mycobacteria Von Willebrand factor domain function, especially in colony morphology and biofilm development.

L-Alanine specifically potentiates fluoroquinolone efficacy against Mycobacterium persisters via increased intracellular reactive oxygen species.

Tuberculosis caused by Mycobacterium tuberculosis remains a major global health concern; M. tuberculosis drug resistance and persistence further fueled the situation. Nutrient supportive therapy was intensively pursued to complement the conventional treatment, as well as their synergy with current antibiotics. To explore whether L-alanine can synergize with fluoroquinolones against M. tuberculosis, M. smegmatis was used as a surrogate in this study. We found that L-alanine can boost the bactericidal efficacy of fluoroquinolones, increasing the production of intracellular reactive oxygen species. This effect is very significant for persisters. Accelerated tricarboxylic acid cycle and/or nucleotide metabolism were observed after the addition of L-alanine. M. smegmatis MSMEG2660 is a homolog of the alanine dehydrogenase (Rv2780, MSMEG2659) negative regulator Rv2779c and involved in the L-alanine potentiation of fluoroquinolone via funneling more alanine into tricarboxylic acid. Deletion mutant of the MSMEG2660 (∆Ms2660) became more susceptible, and more readily revived from persistence. We firstly found that L-alanine can synergize with fluoroquinolones against Mycobacterium, especially the persisters via promoting metabolism. This will inspire new avenue to eliminate Mycobacterium persisters.

Mycobacterium tuberculosis Rv0426c promotes recombinant mycobacteria intracellular survival via manipulating host inflammatory cytokines and suppressing cell apoptosis.

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb) is still a leading cause of death worldwide. M. tuberculosis has evolved multipronged strategies to subvert host immune defenses and establish an immunologically privileged niche in macrophages. Rv0426c has been predicted to be an effector involved in the Mtb-host interactions. To investigate the potential role played by Rv0426c, we constructed recombinant M. smegmatis strains with heterologous expression of Rv0426c. We observed that Rv0426c recombinants became more susceptible to various stresses by increasing cell wall permeability, however with elevated early survival rate within macrophages. This was accompanied by decreased levels of pro-inflammatory cytokines and host cell apoptosis. The data suggested that Rv0426c was a new player involved in the interactions between Mtb and macrophages.

Role of two-component regulatory systems in intracellular survival of Mycobacterium tuberculosis.

The typical two-component regulatory systems (TCSs), consisting of response regulator and histidine kinase, play a central role in survival of pathogenic bacteria under stress conditions such as nutrient starvation, hypoxia, and nitrosative stress. A total of 11 complete paired two-component regulatory systems have been found in Mycobacterium tuberculosis, including a few isolated kinase and regulatory genes. Increasing evidence has shown that TCSs are closely associated with multiple physiological process like intracellular persistence, pathogenicity, and metabolism. This review gives the two-component signal transduction systems in M. tuberculosis and their signal transduction roles in adaption to the environment.

Mce-associated protein Rv0177 alters the cell wall structure of Mycobacterium smegmatis and promotes macrophage apoptosis via regulating the cytokines.

The success of Mycobacterium tuberculosis as a pathogen largely contributes to its ability to infect, modify and persist within the host cells. M. tuberculosis Rv0177 is a gene of the mce1 operon (Mammalian cell entry), encoding a conserved hypothetical protein, essential for M. tuberculosis survival and up-regulated within murine macrophages. To explore its function, Rv0177 was heterologously expressed in M. smegmatis. The recombinant protein was located in the cell wall. M. smegmatis recombinant strain expressing Rv0177 altered sliding motility, its cell wall architecture and the permeability. Moreover, M. smegmatis expressing Rv0177 could up-regulate MCP-1 and downregulate the IL-6 expression in RAW264.7 macrophages in comparison to the control. MS_Rv0177 increased the expression of MCP-1 inducible protein (MCPIP) and a C/EBP homologous protein (CHOP) owing to MCP-1. In addition, the JNK signaling pathway was engaged in the interplay between MS_Rv0177 and macrophages. The macrophage caspase-3 activation and cell apoptosis were induced by the recombinant. This provided novel functional cues for the MCE-associated Rv0177.

Clinical Analysis of Unicentric Castleman's Disease with Paraneoplastic Pemphigus and Bronchiolitis Obliterans.

Objective To investigate the clinical features of unicentric Castleman's disease(UCD)with paraneoplastic pemphigus(PNP)and bronchiolitis obliterans(BO).Method Data of UCD patients with PNP and BO from Peking Union Medical College Hospital were retrospectively analyzed,along with literatures review. Results Totally 23 cases(11 males and 12 females)were enrolled.The median age was 31 years(13-56 years).The most common pathological type was hyaline-vascular variant(91.4%),and most tumors located in abdominopelvic cavity(69.6%).Considerable cases presented bulky masses(26.3%).Most cases were first diagnosed on presentation with the symtoms of PNP(90.0%).BO was characterized by progressive dyspnea after excision of CD lesions.The average follow-up duration was 27.5 months(1-135 months).The median overall survival time was 36.0 months(95% CI=13.9-58.1).Respiratory failure was the dominant cause of death(91.7%).Conclusions PNP should be considered among those patients with specific oral or cutaneous lesions.Earlier diagnosis and treatment of latent UCD are important for reducing complications and deaths.

VUV photo-processing of PAH cations: quantitative study on the ionization versus fragmentation processes.

Interstellar polycyclic aromatic hydrocarbons (PAHs) are strongly affected by the absorption of vacuum ultraviolet (VUV) photons in the interstellar medium (ISM), yet the branching ratio between ionization and fragmentation is poorly studied. This is crucial for the stability and charge state of PAHs in the ISM in different environments, affecting in turn the chemistry, the energy balance, and the contribution of PAHs to the extinction and emission curves. We studied the interaction of PAH cations with VUV photons in the 7 - 20 eV range from the synchrotron SOLEIL beamline, DESIRS. We recorded by action spectroscopy the relative intensities of photo-fragmentation and photo-ionization for a set of eight PAH cations ranging in size from 14 to 24 carbon atoms, with different structures. At photon energies below ~13.6 eV fragmentation dominates for the smaller species, while for larger species ionization is immediately competitive after the second ionization potential (IP). At higher photon energies, all species behave similarly, the ionization yield gradually increases, leveling off between 0.8 and 0.9 at ~18 eV. Among isomers, PAH structure appears to mainly affect the fragmentation cross section, but not the ionization cross section. We also measured the second IP for all species and the third IP for two of them, all are in good agreement with theoretical ones confirming that PAH cations can be further ionized in the diffuse ISM. Determining actual PAH dication abundances in the ISM will require detailed modeling. Our measured photo-ionization yields for several PAH cations provide a necessary ingredient for such models.

The clinical spectrum of IgM monoclonal gammopathy: A single center retrospective study of 377 patients.

OBJECTIVES: We retrospectively evaluated the clinical features, serum levels of IgM, and prevalence of IgM related diseases in patients with serum immunofixation electrophoresis (sIFE) confirmed IgM monoclonal gammopathy at our center. METHODS: We included patients with sIFE confirmed IgM monoclonal gammopathy between January 2008 and December 2014 in this retrospective study. We evaluated clinical data, sIFE, serum IgM levels, and diagnosis. RESULTS: In total, 7107 patients had sIFE confirmed monoclonal gammopathy, with 377 (5.3%) patients having the IgM type. The median age was 62 years (range, 19-105 years). The median level of serum IgM is 8.3g/L (range, 0.24-150g/L). The diagnosis included monoclonal gammopathy of undetermined significance (MGUS, 157 patients, 41.6%), Waldenstrom macroglobulinemia (WM, 105 patients, 27.9%), B cell non-Hodgkin's lymphoma (69 patients, 18.3%), primary cold agglutinin disease (pCAD, 16 patients, 4.2%), primary amyloidosis (14 patients, 3.7%), cryoglobulinaemia (six patients, 1.6%), IgM MGUS associated neuropathy (five patients, 1.3%), multiple myeloma (three patients, 0.8%), and POEMS syndrome (two patients, 0.5%). Levels of serum IgM>15.5g/L were 80.6% sensitive and 89.2% specific for the diagnosis of WM. Kappa type light chain indicated the diagnosis of WM, pCAD, IgM MGUS associated neuropathy and cryoglobulinaemia, while lambda type light chain indicated POEMS and amyloidosis. There were 41/157 (26.1%) MGUS patients diagnosed with complications due to IgM-unrelated autoimmune diseases. CONCLUSION: IgM monoclonal gammopathy contains a broad spectrum of diseases. Levels of serum IgM and the type of light chain can be used to help with differential diagnosis. The association between MGUS and some autoimmune diseases requires further investigation.

An optical spectrum of a large isolated gas-phase PAH cation: C78H26.

A gas-phase optical spectrum of a large polycyclic aromatic hydrocarbon (PAH) cation - C78H26+- in the 410-610 nm range is presented. This large all-benzenoid PAH should be large enough to be stable with respect to photodissociation in the harsh conditions prevailing in the interstellar medium (ISM). The spectrum is obtained via multi-photon dissociation (MPD) spectroscopy of cationic C78H26 stored in the Fourier Transform Ion Cyclotron Resonance (FT-ICR) cell using the radiation from a mid-band optical parametric oscillator (OPO) laser. The experimental spectrum shows two main absorption peaks at 431 nm and 516 nm, in good agreement with a theoretical spectrum computed via time-dependent density functional theory (TD-DFT). DFT calculations indicate that the equilibrium geometry, with the absolute minimum energy, is of lowered, nonplanar C2 symmetry instead of the more symmetric planar D2h symmetry that is usually the minimum for similar PAHs of smaller size. This kind of slightly broken symmetry could produce some of the fine structure observed in some diffuse interstellar bands (DIBs). It can also favor the folding of C78H26+ fragments and ultimately the formation of fullerenes. This study opens up the possibility to identify the most promising candidates for DIBs amongst large cationic PAHs.

LABORATORY PHOTO-CHEMISTRY OF PAHS: IONIZATION VERSUS FRAGMENTATION.

Interstellar Polycyclic Aromatic Hydrocarbons (PAH) are expected to be strongly processed by Vacuum Ultra-Violet (VUV) photons. Here, we report experimental studies on the ionization and fragmentation of coronene (C24H12), ovalene (C32H14) and hexa-peri-hexabenzocoronene (HBC; C42H18) cations by exposure to synchrotron radiation in the range of 8-40 eV. The results show that for small PAH cations such as coronene, fragmentation (H-loss) is more important than ionization. However, as the size increases, ionization becomes more and more important and for the HBC cation, ionization dominates. These results are discussed and it is concluded that, for large PAHs, fragmentation only becomes important when the photon energy has reached the highest ionization potential accessible. This implies that PAHs are even more photo-stable than previously thought. The implications of this experimental study for the photo-chemical evolution of PAHs in the interstellar medium (ISM) are briefly discussed.

Photolysis of n-butyl nitrite and isoamyl nitrite at 355 nm: a time-resolved Fourier transform infrared emission spectroscopy and ab initio study.

We report on the photodissociation dynamics study of n-butyl nitrite and isoamyl nitrite by means of time-resolved Fourier transform infrared (TR-FTIR) emission spectroscopy. The obtained TR-FTIR emission spectra of the nascent NO fragments produced in the 355 nm laser photolysis of the two alkyl nitrite species showed an almost identical rotational temperature and vibrational distributions of NO. In addition, a close resemblance between the two species was also found in the measured temporal profiles of the IR emission of NO and the recorded UV absorption spectra. The experimental results are consistent with our ab initio calculations using the time-dependent density functional theory at the B3LYP/6-311G(d,p) level, which indicate that the substitution of one of the two gamma-H atoms in n-C(4)H(9)ONO with a methyl group to form (CH(3))(2)C(3)H(5)ONO has only a minor effect on the photodissociation dynamics of the two molecules.